GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lysP in Pseudomonas fluorescens FW300-N2E2

Align The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized)
to candidate Pf6N2E2_5459 D-serine/D-alanine/glycine transporter

Query= TCDB::K7VV21
         (488 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5459
           D-serine/D-alanine/glycine transporter
          Length = 473

 Score =  309 bits (791), Expect = 2e-88
 Identities = 180/462 (38%), Positives = 268/462 (58%), Gaps = 23/462 (4%)

Query: 13  VKRGLKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMVYFLMTSLGEM 72
           +KR L  RH+ ++ALG  IG GLFL S   I  AGP   + +Y++ G  +  +M +LGEM
Sbjct: 18  LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGP-AIMLSYIIGGLAILVIMRALGEM 76

Query: 73  ATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIKFWLPDVPSWI 132
           A + P +GSFS Y   Y+ P  GF  GWNYW  W +T   ++TAVA+ +  W PDVP WI
Sbjct: 77  AVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWI 136

Query: 133 FSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLIIGFLSIFGIMGGHIDVAKNL 192
           ++L AL+ + SIN ++VK FGE E+W + IKI V ++ ++IG + I     G+  VA  +
Sbjct: 137 WALAALVSMGSINLIAVKAFGEFEFWFALIKI-VTIIAMVIGGVGIIAFGFGNDGVALGI 195

Query: 193 S-VGNHGFVGGLGSFTTGG--GILGVLLVAGFSFQGTELLGITAGEAENPEKSIPKAMNS 249
           S +  H      G F   G  G+L  L +  F++ G E++G+TAGEA+NP+K+IP A+ S
Sbjct: 196 SNLWTH------GGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGS 249

Query: 250 IFWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIAASIMNAVVLT 309
           +FWRIL+FY+ ++FV+ +I P+ +    G      SPF + FER+G   AA I+N VV+T
Sbjct: 250 VFWRILLFYVGALFVILSIYPWNEIGTQG------SPFVMTFERLGIKTAAGIINFVVIT 303

Query: 310 SVVSAANSGMYASTRMLYSLAKDGGAPTIFSKTSKNGIPFIALLATTAVALL-TFLTSIY 368
           + +S+ N G++++ RMLYSLA++G AP  F+ TS NG+P  ALL + A  LL   L  + 
Sbjct: 304 AALSSCNGGIFSTGRMLYSLAQNGQAPAGFATTSANGVPRRALLLSIAALLLGVLLNYLV 363

Query: 369 GVSFFTFLVSASGLTGFIAWIGIAISHFRFRRAYVAQGKDVKKLPYHAKLFPFGPILALI 428
               F ++ S +       W+ I ++  +FR++  A  +    L Y   L+P    LAL 
Sbjct: 364 PEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASER--AALKYRMWLYPVSSYLALA 421

Query: 429 MTVLVTLGQDPMLLFGKTWVQGVVMYAAIPLFFILYLGYKFK 470
             VLV      M  F  T V   V  A + L  +L+  +K +
Sbjct: 422 FLVLVV---GLMAYFPDTRVALYVGPAFLVLLTVLFYVFKLQ 460


Lambda     K      H
   0.326    0.141    0.425 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 583
Number of extensions: 24
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 488
Length of database: 473
Length adjustment: 34
Effective length of query: 454
Effective length of database: 439
Effective search space:   199306
Effective search space used:   199306
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory